Mercurial > repos > computational-metabolomics > mspurity_createdatabase
view createDatabase.R @ 2:a11892cb997d draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
author | computational-metabolomics |
---|---|
date | Wed, 01 Apr 2020 11:17:09 -0400 |
parents | f52287a06c02 |
children | 3d36a391612c |
line wrap: on
line source
library(msPurity) library(optparse) library(xcms) library(CAMERA) print(sessionInfo()) print('CREATING DATABASE') xset_pa_filename_fix <- function(opt, pa, xset){ if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){ # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables # needs to be done due to Galaxy moving the files around and screwing up any links to files filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) filepaths <- filepaths[filepaths != ""] new_names <- basename(filepaths) galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) galaxy_names <- galaxy_names[galaxy_names != ""] nsave <- names(pa@fileList) old_filenames <- basename(pa@fileList) pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] names(pa@fileList) <- nsave pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) } if(!all(basename(pa@fileList)==basename(xset@filepaths))){ if(!all(names(pa@fileList)==basename(xset@filepaths))){ print('FILELISTS DO NOT MATCH') message('FILELISTS DO NOT MATCH') quit(status = 1) }else{ xset@filepaths <- unname(pa@fileList) } } print(xset@phenoData) print(xset@filepaths) return(list(pa, xset)) } option_list <- list( make_option(c("-o", "--outDir"), type="character"), make_option("--pa", type="character"), make_option("--xset_xa", type="character"), make_option("--xcms_camera_option", type="character"), make_option("--eic", action="store_true"), make_option("--cores", default=4), make_option("--mzML_files", type="character"), make_option("--galaxy_names", type="character"), make_option("--grpPeaklist", type="character") ) # store options opt<- parse_args(OptionParser(option_list=option_list)) print(opt) loadRData <- function(rdata_path, name){ #loads an RData file, and returns the named xset object if it is there load(rdata_path) return(get(ls()[ls() %in% name])) } getxcmsSetObject <- function(xobject) { # XCMS 1.x if (class(xobject) == "xcmsSet") return (xobject) # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object suppressWarnings(xset <- as(xobject, 'xcmsSet')) sampclass(xset) <- xset@phenoData$sample_group return (xset) } } print(paste('pa', opt$pa)) print(opt$xset) print(opt$xcms_camera_option) # Requires pa <- loadRData(opt$pa, 'pa') print(pa@fileList) if (opt$xcms_camera_option=='xcms'){ xset <- loadRData(opt$xset, c('xset','xdata')) xset <- getxcmsSetObject(xset) fix <- xset_pa_filename_fix(opt, pa, xset) pa <- fix[[1]] xset <- fix[[2]] xa <- NULL }else{ xa <- loadRData(opt$xset, 'xa') fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet) pa <- fix[[1]] xa@xcmsSet <- fix[[2]] xset <- NULL } if(is.null(opt$grpPeaklist)){ grpPeaklist = NA }else{ grpPeaklist = opt$grpPeaklist } dbPth <- msPurity::createDatabase(pa, xset=xset, xsa=xa, outDir=opt$outDir, grpPeaklist=grpPeaklist, dbName='createDatabase_output.sqlite' ) if (!is.null(opt$eic)){ if (is.null(xset)){ xset <- xa@xcmsSet } # previous check should have matched filelists together xset@filepaths <- unname(pa@fileList) convert2Raw <- function(x, xset){ sid <- unique(x$sample) # for each file get list of peaks x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])] x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])] x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])] return(x) } xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset)) # Saves the EICS into the previously created database px <- msPurity::purityX(xset, saveEIC = TRUE, cores=1, sqlitePth=dbPth, rtrawColumns = TRUE) } closeAllConnections()